The NHGRI-EBI GWAS Catalog is a publicly available resource of Genome Wide Association Studies (GWAS) and their results. This course provides an introduction of how to browse SNP-trait associations using the NHGRI-EBI GWAS Catalog.

By the end of the course you will be able to:
recall the purpose and function of the NHGRI-EBI GWAS Catalog
recall the type and scope of the data which it contains
search the Catalog to identify variants associated with particular traits
know where to get help and support on the GWAS Catalog

Genome3D provides consensus structural annotations and 3D models for sequences from ten model organisms, including human. These data are generated by several UK-based resources that together form the Genome3D consortium: SCOP, CATH, SUPERFAMILY, Gene3D, FUGUE, pDomTHREADER and PHYRE. InterPro, meanwhile, provides functional analysis of proteins by classifying them into homologous superfamilies and families, and by predicting domains, repeats and important sites, based on data from 14 member databases.

This webinar presents the new InterPro entry type, Homologous superfamily, as well as describing domain and structure predictions from Genome3D annotations, and how they are integrated in InterPro.

Who is this course for?
This webinar is aimed at individuals working with variation data who wish to learn about Genome3D and InterPro's Homologous superfamily. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of biology would be useful.

The new Genome3D annotations provide information on the likely structure of proteins, and the predictions made can guide the design of protein constructs for structural studies.

By the end of the course you will be able to:
explain the role of Genome3D annotations in InterPro

This quick tour provides a brief introduction to Genome Properties, a resource for assigning pathway function to species based on the presence or absence of defined molecular markers, as detected by the protein signature models contained within InterPro.

By the end of the course you will be able to:
Describe the data contained in Genome Properties
Summarise how Genome Properties data can be accessed

Genome Properties allows you to infer the presence of pathways and systems within a species, based on the occurrence of a set of underlying molecular markers.

By the end of the course you will be able to:
Describe the data contained in Genome Properties
Demonstrate various ways to search the resource
Propose ways to use Genome Properties in your own research

Gene expression is controlled by a complicated network of transcription factors and repressors, interacting with genomic features such as promoters and enhancers, dependant on epigenetic marks at those loci. Ensembl provides access to epigenomic data on histone modifications and protein binding across the genome, integrated with data on genes and genetic variation.

Join Ensembl to investigate a genomic region which controls gene expression, determine its activity in different cell types and view the epigenomic markers at that locus, plus see how to access these data in bulk.

Who is this course for?
No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

A cornerstone of modern molecular biology is the electronic transfer of annotations form a few experimentally characterised sequences to the vast number being determined from DNA modern sequencing technologies. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software and associated website housed at EMBL-EBI, which in the latest version, uses a combination of sophisticated acceleration heuristics and mathematical and computational optimisations to enable the use of profile hidden Markov models (HMMs) for sequence analysis.

In this webinar, we will cover some of the basics about the HMMER algorithm and the use of the HMMER via the website.

Who is this course for?
This webinar is aimed at individuals who wish to learn more about the HMMER. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

Understanding protein functions is crucial to unlocking the value of genomic data for biomedical research and innovation. Delivering personalised health and precision medicine requires a detailed understanding of the consequences of sequence variants in proteins and their impact on phenotype. The widening gap between known proteins and their functions has encouraged the development of methods to automatically infer annotations. Artificial intelligence and machine learning hold a large repertoire of algorithms and methodologies to discover and infer prediction models. Coupled with the new big data technologies for interactive analytics and data transformation, the AI/ML methods represent valuable assets that could enhance the discovery of protein functions.

This tutorial will help you understanding how to use Spark and Interactive Analytics to make sense of protein data and build machine learning models to infer their functions.

Who is this course for?
Scientists and bioinformaticians with an interest in protein functions, machine learning and modelling.

This webinar will introduce AlphaFold system for prediction and interpretation of protein structures. This webinar is designed for experimental biologists who wish to understand the strengths and limitations of AlphaFold and use the models to guide their experimental studies.

In this webinar we will provide an overview for the AlphaFold method and statistics that can be used to understand the reliability of the models. We will also introduce the AlphaFold Database, which provides hundreds of thousands of ready-made models across the tree of life, as well as highlight the AlphaFold Open Source and Colab notebooks that can be used to generate structures of sequences not yet available within the AlphaFold Database.

We will conclude by demonstrating a range of use cases followed by a question and answer session with all the presenters.

Who is this course for?
This webinar is suitable for lab-based and computational researchers with an interest in structural biology.

Outcomes
By the end of the webinar you will be able to:

Explain basic principles of how AlphaFold 2.0 works
Discuss how to interpret the results of AlphaFold
Identify where to find AlphaFold models at EMBL-EBI
Explore how to easily create AlphaFold models using Open source and Google Colab

There is a wealth of training content developed and delivered across the globe each year, there will be many similar sessions on similar topics all delivered to similar audiences. At the same time, there will be trainers looking for inspiration and ideas on how to approach new topics or on new ways to teach old topics; as well as trainees looking for materials to further their own knowledge. Many trainers (or lecturers/educators etc) do not share their materials, or if materials are shared they are not easily found or re-used by others.

During this webinar, we will give you some tips and suggestions on how you can make more of the training materials you produce and encourage others to do the same. FAIR is not just for data - we can make our training materials FAIR too. Join us to find out the benefits of sharing your FAIR materials and some simple ways you can make it easy for others to use your materials in their teaching, or as aids for individuals to learn more.

The “How FAIR are you” webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.

Who is this course for?
This webinar is for anyone who is interested in applying FAIR principles to training materials; no prior skills are required.

Though text mining becomes more widespread in biology, an average researcher can rarely use it to their advantage. In this webinar Europe PMC presents a tool to easily share annotated biological entities and relations with the research community. Europe PMC Annotation Submission System allows text miners and curators in the field of life sciences to make their results available to the public. Annotated concepts can be browsed and searched for both on Europe PMC website as a part of SciLite tool and Advanced search, as well as via the Annotations API.

Who is this course for?
This webinar is aimed at individuals who wish to learn more about sharing and reusing results of biomedical text-mining. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

Genetic variation is fundamental to the evolution of all species and is what makes us individuals. This course focuses on heritable variation and will give you a taste of the resources you can use to explore genetic variation data.

By the end of the course you will be able to:
Review sources of genetic variation
Describe the possible effects of genetic variation
Identify common genetic variation file types and formats
Describe types of genetic variation studies

Genetic variation is fundamental to the evolution of all species and is what makes us individuals. Our genes have a large influence on our lives. They affect what we look like, our personalities and preferences and our susceptibility to disease. By studying genetic variation we hope to understand the molecular processes that contribute to life on earth.

By the end of the course you will be able to:
List examples of genetic variation databases
Describe the type of data found in different genetic variation databases
Explore genetic variation data within publicly available resources

This quick tour provides a brief introduction to the EMBL-EBI's molecular interactions database, IntAct.

By the end of the course you will be able to:
Describe IntAct and how it can help you to find information on molecular interactions
Explore where to find out more about IntAct

A complete understanding of biological systems requires integration of knowledge of the regulation and function of small molecule metabolites – the metabolome – with that of genes, transcripts, and proteins (the genome, transcriptome, and metabolome).

The UniProt knowledgebase UniProtKB supports biomedical research by providing a comprehensive, high quality and freely accessible resource of protein sequences and functional information. UniProtKB integrates, interprets and standardizes data from a range of sources including the scientific literature, tools for protein sequence analysis, other knowledge resources and databases, and automatic annotation systems, to provide a detailed overview of the available protein knowledge.

This webinar will provide an introduction into how UniProtKB captures and represents knowledge of small molecule metabolites using the Rhea knowledgebase of biochemical reactions, based on the chemical ontology ChEBI, and how UniProt users can access and exploit that knowledge.

Who is this course for?
This webinar targets life scientists and bioinformaticians who study enzymes and small molecules, particularly those interested in linking or bridging the two domains. No prior knowledge of bioinformatics or cheminformatics is required, but an undergraduate level knowledge of biology/ biochemistry would be useful.

Outcomes
By the end of the webinar you will be able to:

Describe how UniProt annotates enzyme and transporter function, and where the data comes from
Find and retrieve information about specific enzymes, transporters and the metabolites on which they act, by searching UniProtKB using text, chemical structures, and chemical classifications
Help us develop the representation of small molecule data in UniProtKB by providing valuable feedback

Research literature contains a wealth of information that can be extracted at scale using text-mining technologies. To make text-mining data available to a wider group of researchers, the publications database, Europe PMC, provides access to millions of text-mined annotations, such as genes and proteins, metabolites, species, mutations, phosphorylations, interactions, associations, and many more.

This webinar will demonstrate how to access text-mined literature evidence programmatically, and how to supplement it with bibliographic information for advanced use cases. Two of such use cases, mapping of tropical disease research by author affiliation geoparsing and comparison of applicability of analytical chemistry techniques, will be introduced by invited speaker, Dr. Magnus Palmblad.

Who is this course for?
This webinar is aimed at individuals who wish to learn about accessing text-mined literature evidence programmatically. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of biology would be useful.

This course provides an insight into the different protein family building methodologies employed by three InterPro member databases, namely SFLD (Structure Function Linkage Database), TIGRFAMs and PANTHER. It also describes an automated approach to comparing protein signatures and predicting hierarchical relationships between them.

By the end of the course you will be able to:
Identify differences and similarities in methodologies of protein signature creation by SFLD, TIGRFAMs and PANTHER
Illustrate how protein signatures can be compared to predict relationships between them

InterPro is a classification database that provides predictive information about protein sequences.

By the end of the course you will be able to:
search the InterPro database in a number of different ways
interpret the information in an InterPro entry page
review the graphical representation of the signature matches on an InterPro protein page

This quick tour provides a brief introduction to InterPro, EMBL-EBI's database of protein families, domains and functional sites.

By the end of the course you will be able to:
explain what InterPro is and how it can help you to relate protein architecture to function
determine where to find out more about InterPro

This webinar is about InterProScan, the underlying software application that scans both protein and nucleic acid sequences against InterPro's predictive models, which are provided by the InterPro’s member databases. InterPro is a freely available resource used to classify sequences into protein families and to predict the presence of important domains and sites.

Who is this course for?
This webinar is aimed at scientists and bioinformaticians with an interest in using InterProScan for protein functional analysis or anyone with interest in protein sequence annotation using InterPro. A basic knowledge of using the command line interface is recommended for this webinar.